GSvar: added check that WES/WGS samples were loaded completely.

Author: marc-sturm

doc/tools/CnvFilterAnnotations.md

@@ -1,5 +1,5 @@
 ### CnvFilterAnnotations tool help
-	CnvFilterAnnotations (2020_03-184-g27235379)
+	CnvFilterAnnotations (2021_06-89-gbbd16264)
 
 	Filter a copy-number variant list in TSV format based on variant annotations.
 
@@ -27,7 +27,7 @@
 	                             mode - Compound-heterozygotes detection mode. [default=n/a] [valid=n/a,CNV-CNV,CNV-SNV/INDEL]
 	CNV copy-number            Filter for CNV copy number.
 	                           Parameters:
-	                             cn - Copy number [default=n/a] [valid=n/a,0,1,2,3,4+]
+	                             cn - Copy number [valid=0,1,2,3,4,5+] [non-empty]
 	CNV gene constraint        Filter based on gene constraint (gnomAD o/e score for LOF variants).
 	                           Note that gene constraint is most helpful for early-onset severe diseases.
 	                           For details on gnomAD o/e, see https://macarthurlab.org/2018/10/17/gnomad-v2-1/
@@ -82,7 +82,7 @@
 	  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### CnvFilterAnnotations changelog
-	CnvFilterAnnotations 2020_03-184-g27235379
+	CnvFilterAnnotations 2021_06-89-gbbd16264
 
 	2020-05-25 Initial version of the tool. Based on VariantFilterAnnotations.
 [back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/MappingQC.md

@@ -1,5 +1,5 @@
 ### MappingQC tool help
-	MappingQC (2020_12-85-g5ff87d17)
+	MappingQC (2021_06-89-gbbd16264)
 
 	Calculates QC metrics based on mapped NGS reads.
 
@@ -28,6 +28,8 @@
 	                  Valid: 'hg19,hg38'
 	  -ref <file>     Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
 	                  Default value: ''
+	  -cfdna          Add additional QC parameters for cfDNA samples. Only supported mit '-roi'.
+	                  Default value: 'false'
 
 	Special parameters:
 	  --help          Shows this help and exits.
@@ -36,7 +38,7 @@
 	  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### MappingQC changelog
-	MappingQC 2020_12-85-g5ff87d17
+	MappingQC 2021_06-89-gbbd16264
 
 	2021-02-09 Added new QC metrics for uniformity of coverage (QC:2000057-QC:2000061).
 	2020-11-27 Added CRAM support.

doc/tools/NGSDExportAnnotationData.md

@@ -1,34 +1,36 @@
 ### NGSDExportAnnotationData tool help
-	NGSDExportAnnotationData (2021_06-48-gfc326851)
+	NGSDExportAnnotationData (2021_06-89-gbbd16264)
 
 	Generates a VCF file with all variants and annotations from the NGSD and a BED file containing the gene information of the NGSD.
 
 	Mandatory parameters:
-	  -variants <file>   Output variant list as VCF.
+	  -variants <file>      Output variant list as VCF.
 
 	Optional parameters:
-	  -genes <file>      Optional BED file containing the genes and the gene info (only germline).
-	                     Default value: ''
-	  -reference <file>  Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
-	                     Default value: ''
-	  -test              Uses the test database instead of on the production database.
-	                     Default value: 'false'
-	  -max_af <float>    Maximum allel frequency of exported variants (default: 0.05).
-	                     Default value: '0.05'
-	  -gene_offset <int> Defines the number of bases by which the region of each gene is extended.
-	                     Default value: '5000'
-	  -mode <enum>       Determines the database which is exported.
-	                     Default value: 'germline'
-	                     Valid: 'germline,somatic'
+	  -genes <file>         Optional BED file containing the genes and the gene info (only germline).
+	                        Default value: ''
+	  -reference <file>     Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
+	                        Default value: ''
+	  -test                 Uses the test database instead of on the production database.
+	                        Default value: 'false'
+	  -max_af <float>       Maximum allel frequency of exported variants (default: 0.05).
+	                        Default value: '0.05'
+	  -gene_offset <int>    Defines the number of bases by which the region of each gene is extended.
+	                        Default value: '5000'
+	  -mode <enum>          Determines the database which is exported.
+	                        Default value: 'germline'
+	                        Valid: 'germline,somatic'
+	  -vicc_config_details  Includes details about VICC interpretation. Works only in somatic mode.
+	                        Default value: 'false'
 
 	Special parameters:
-	  --help             Shows this help and exits.
-	  --version          Prints version and exits.
-	  --changelog        Prints changeloge and exits.
-	  --tdx              Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
+	  --help                Shows this help and exits.
+	  --version             Prints version and exits.
+	  --changelog           Prints changeloge and exits.
+	  --tdx                 Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### NGSDExportAnnotationData changelog
-	NGSDExportAnnotationData 2021_06-48-gfc326851
+	NGSDExportAnnotationData 2021_06-89-gbbd16264
 
 	2021-07-19 Code and parameter refactoring.
 	2021-07-19 Added support for 'germline_het' and 'germline_hom' columns in 'variant' table.

doc/tools/VcfAnnotateFromBed.md

@@ -1,5 +1,5 @@
 ### VcfAnnotateFromBed tool help
-	VcfAnnotateFromBed (2021_03-100-g09f25a25)
+	VcfAnnotateFromBed (2021_06-89-gbbd16264)
 
 	Annotates the INFO column of a VCF with data from a BED file.
 
@@ -9,26 +9,36 @@
 	 -> %0A;  -> %0D;   -> %20; , -> %2C; ; -> %3B; = -> %3D;
 
 	Mandatory parameters:
-	  -bed <file>    BED file used as source of annotations (name column).
-	  -name <string> Annotation name in INFO column of output VCF file.
+	  -bed <file>       BED file used as source of annotations (name column).
+	  -name <string>    Annotation name in INFO column of output VCF file.
 
 	Optional parameters:
-	  -in <file>     Input VCF file. If unset, reads from STDIN.
-	                 Default value: ''
-	  -out <file>    Output VCF list. If unset, writes to STDOUT.
-	                 Default value: ''
-	  -sep <string>  Separator used if there are several matches for one variant.
-	                 Default value: ':'
+	  -in <file>        Input VCF file. If unset, reads from STDIN.
+	                    Default value: ''
+	  -out <file>       Output VCF list. If unset, writes to STDOUT.
+	                    Default value: ''
+	  -sep <string>     Separator used if there are several matches for one variant.
+	                    Default value: ':'
+	  -threads <int>    The number of threads used to read, process and write files.
+	                    Default value: '1'
+	  -block_size <int> Number of lines processed in one chunk.
+	                    Default value: '5000'
+	  -prefetch <int>   Maximum number of chunks that may be pre-fetched into memory.
+	                    Default value: '64'
+	  -debug <int>      Enables debug output at the given interval in milliseconds (disabled by default, cannot be combined with writing to STDOUT).
+	                    Default value: '-1'
 
 	Special parameters:
-	  --help         Shows this help and exits.
-	  --version      Prints version and exits.
-	  --changelog    Prints changeloge and exits.
-	  --tdx          Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
+	  --help            Shows this help and exits.
+	  --version         Prints version and exits.
+	  --changelog       Prints changeloge and exits.
+	  --tdx             Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### VcfAnnotateFromBed changelog
-	VcfAnnotateFromBed 2021_03-100-g09f25a25
+	VcfAnnotateFromBed 2021_06-89-gbbd16264
 
+	2021-09-18 Prefetch only part of input file (to save memory).
+	2021-08-24 Added multithread support.
 	2021-06-15 Added 'sep' parameter.
 	2019-12-06 Added URL encoding for INFO values.
 	2017-03-14 Initial implementation.

doc/tools/VcfAnnotateFromVcf.md

@@ -1,5 +1,5 @@
 ### VcfAnnotateFromVcf tool help
-	VcfAnnotateFromVcf (2020_03-184-g27235379)
+	VcfAnnotateFromVcf (2021_06-89-gbbd16264)
 
 	Annotates the INFO column of a VCF with data from another VCF file (or multiple VCF files if config file is provided).
 
@@ -24,6 +24,8 @@
 	                          Default value: '1'
 	  -block_size <int>       Number of lines processed in one chunk.
 	                          Default value: '5000'
+	  -prefetch <int>         Maximum number of chunks that may be pre-fetched into memory.
+	                          Default value: '64'
 
 	Special parameters:
 	  --help                  Shows this help and exits.
@@ -32,8 +34,9 @@
 	  --tdx                   Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### VcfAnnotateFromVcf changelog
-	VcfAnnotateFromVcf 2020_03-184-g27235379
+	VcfAnnotateFromVcf 2021_06-89-gbbd16264
 
+	2021-09-20 Prefetch only part of input file (to save memory).
 	2020-04-11 Added multithread support by Julian Fratte.
 	2019-08-19 Added support for multiple annotations files through config file.
 	2019-08-14 Added VCF.GZ support.

src/GSvar/MainWindow.cpp

@@ -2834,10 +2834,30 @@ void MainWindow::checkVariantList(QStringList messages)
 		}
 	}
 
+	//check data was loaded completely
+	if (germlineReportSupported(true))
+	{
+		NGSD db;
+		int sys_id = db.processingSystemIdFromProcessedSample(germlineReportSample());
+		ProcessingSystemData sys_data = db.getProcessingSystemData(sys_id);
+		if (sys_data.type=="WES" || sys_data.type=="WGS")
+		{
+			QSet<Chromosome> chromosomes;
+			for(int i=0; i<variants_.count(); ++i)
+			{
+				chromosomes << variants_[i].chr();
+			}
+			if (chromosomes.size()<23)
+			{
+				messages << ("Variants detected on " + QString::number(chromosomes.size()) + " chromosomes only! Expected variants on at least 23 chromosomes for WES/WGS data!");
+			}
+		}
+	}
+
 	//show messages
 	if (!messages.empty())
 	{
-		QMessageBox::warning(this, "GSvar file outdated", "The GSvar file contains the following error(s):\n  -" + messages.join("\n  -") + "\n\nTo ensure that GSvar works as expected, re-run the annotation steps for the analysis!");
+		QMessageBox::warning(this, "GSvar file problems", "The GSvar file contains the following problems:\n  -" + messages.join("\n  -"));
 	}
 }